Nutrient availability coordinates global patterns of bacterial gene expression as well as pathway-specific regulation. These complex networks ultimately involve coordinate regulation of expression of the genomic repertoire as well as macromolecular synthesis. This project focuses on the role of two analogs of GDP and GTP containing an esterified pyrophosphate on the ribose 3'-hydroxyl, collectively abbreviated as (p)ppGpp. Responses to nutrient limitation involve fluctuations in levels of (p)ppGpp, whether starving for amino acids, phosphate, nitrogen or energy sources. This fluctuation is a key element in the ensuing adaptive responses. Most such responses are thought to occur at the transcriptional level yet documentation of in vitro effects of (p)ppGpp on transcription has remained elusive. An alternative genetic approach has previously led to isolation of over 50 mutants of RNA polymerase in rpoB, C & D subunit genes that suppress cellular phenotypes associated with a deficiency of (p)ppGpp. Sites of these amino acid changes have now been mapped as exclusively localized on enzyme surfaces deduced to involve DNA contacts. This is of interest because (p)ppGpp does not affect DNA binding by appropriately regulated promoters. Most eubacteria contain a single bifunctional enzyme capable of both (p)ppGpp synthesis and (p)ppGpp degradation. In contrast, E. coli contains two essentially monofunctional enzymes, each dedicated to an opposing activity. Using chimeras, we have demonstrated fundamental similarities between the domains of a bifunctional enzyme from Streptococcus and the two monofunctional domains of evolutionarily distant E. coli. This finding implies that the widespread bacterial (p)ppGpp regulatory system originates from a single gene family which could provide an attractive target for antibacterial drug.